IlluminaCompute Unveiled at Bio-IT World Europe

November 10, 2009 | HANNOVER—A three-way partnership between Illumina, Dell, and Isilon Systems has resulted in IlluminaCompute, a fully integrated computing solution for Illumina’s best-selling GA II next-generation sequencing instrument. The announcement was made by Dirk Evers, director of computational biology at Illumina, at the inaugural Bio-IT World Europe Conference* in October.

Evers described IlluminaCompute as “an informatics ecosystem for production-scale sequencing.” Illumina elected to partner with blade servers from Dell and modular IQ storage from Isilon Systems. “We made the decision to find partners that we trust to deliver good performance. We have exceptional relations with Isilon and Dell… It is essentially the same system that we use internally, and it works for us,” he said.

The resulting system offers a flexible and scalable system for high-throughput genome analysis, providing a centralized high-performance computational and storage infrastructure. The solution will be launched this winter in three tiers—tier 0, tier 1 and tier 2. Pricing has still to be determined.

IlluminaCompute satisfies an unmet need for scalable computing capabilities that can match the increasing throughput of the GA instrument, commented Illumina’s VP and CIO Scott Kahn. “No other genomics provider currently offers a turnkey solution like IlluminaCompute that can be customized for small and growing sequencing facilities and scaled to meet the needs of larger genome centers.”

Illumina says it will validate the prospective site before installation. Advantages of the system include scalability, provision of centralized high performance, and reduction in support overhead, an important financial factor. IlluminaCompute is plug-and-play with low power consumption, and can be easily reconfigured as researchers’ computing needs change.

Evers, who runs a software group that writes the image analysis, base calling, and mapping software for the GA pipeline, says IlluminaCompute is a response to the remarkable growth of the sequencing market and the throughput of each machine. Illumina has doubled the output of the GA instrument in the past year through various reagent, engineering and software enhancements.

Evers pointed out that Illumina has already migrated much of the storage and compute to the instrument to enable customers “to get at the fundamentals of the data, base calls and quality scores.” By pushing the efficiency of the computing algorithms, all of the computing algorithms can be run in real time on a regular 4-core PC next to the GA II instrument. But as the sequence yield grows, users “need to do the bioinformatics analysis on the data to get at the biologically meaningful results. Now that’s not something you can make go away, because of the increasing volume of sequencers… That’s where you should spend the money.”

Three’s Company
Evers says the choice of Dell and Isilon was in part dedicated by Illumina’s own internal satisfaction with their systems. “It’s natural to then go with the vendor you’re using internally, but it’s not that we didn’t talk to other people,” Evers said. “Of course, we explore the space, but we still came up with the same answer,” says Evers. “You talk to multiple customers and you see the comments they made. We’re still in the situation that we came up with the right partner, which is quite telling in this fast moving space.”

Chris Blessington, Isilon director of marketing, added: “We’re terrifically interested in the business outcome of this partnership, both for Illumina’s ability to serve their customers, and as a business proposition for us. But what it is really, primarily, is the utmost validation that the data storage challenges experienced by these large and growing sequencing endeavors are a match made in heaven for the hallmark attributes of Isilon’s architecture.”

The Illumina GA II is the main workhorse at four of the world’s leading genome centers—the Broad Institute, The Genome Center at Washington University, the Wellcome Trust Sanger Institute, and the Beijing Genomics Institute, Shenzhen (see, p. 20), boast fleets of dozens of GA II instruments. According to the Broad’s Matthew Trunnell, also speaking at Bio-IT World Europe, the Broad currently has 59 Illumina GA II’s in production, with more to come.

But Evers says the target market for IlluminaCompute really focuses on organizations deploying a single sequencer to 5-10 instruments, rather than the major genome centers running fleets of GA machines. “Most purchases are single-instrument purchases now,” says Evers. “That is where you need to come up with this kind of offering.”

“There’s a huge swath of opportunities from single sequencer to 5, 10, maybe more, for many organizations that are data-rich and IT-light, and in many cases getting data richer and IT lighter,” adds Isilon’s Blessington. “The cost pressures on these organizations are no different than commercial enterprises. As the data pressures continue to grow and the ability to support it through IT operational costs and people continue to get tighter, that’s really the market segment here. It’s tough to put a number on it.”